S143: TRANSCRIPTOMIC CHARACTERIZATION OF MRD RESPONSE AND NON-RESPONSE IN PATIENTS TREATED WITH FIXED-DURATION VENETOCLAX-OBINUTUZUMAB
Authors: O. Al-Sawaf, H. Y. Jin, C. Zhang, Y. Choi, S. Balasubramanian, S. Robrecht, A. Kotak, N. Chang, A.-M. Fink, E. Tausch, C. Schneider, M. Ritgen, K.-A. Kreuzer, B. Chyla, J. Paulson, B. Eichhorst, S. Stilgenbauer, Y. Jiang, M. Hallek, K. Fischer
Journal: HemaSphere (2022)

Background: Minimal residual disease (MRD) is a key surrogate for the depth of remission of CLL. The highest rates of undetectable MRD have been observed with regimens using the BH3 mimetic venetoclax. In CLL14, most patients (pts) receiving venetoclax-obinutuzumab (Ven-Obi) had undetectable MRD (uMRD <10-4) at the end of treatment (EoT). However, a subgroup of pts remained MRD positive, regardless of TP53 aberrations or unmutated IGHV status. The biological drivers of response or non-response have so far not been elucidated. Aims: This study explores whether differential transcriptomic profiles can discriminate between pts with vs without deep MRD remissions, particularly after Ven exposure. This might eventually allow for biology-informed treatment development for pts in this high-risk disease setting. Methods: NGS-based MRD measurements (clonoSEQ) from peripheral blood (PB) at follow-up month 3 were grouped into uMRD <10-6 (MRD6), 10-6 ≤ and <10-4 (MRD4/5), and detectable MRD ≥10-4 (MRD+). Pre-treatment CD19-enriched PB samples, and samples collected at relapse from a subset of pts, were subjected to bulk RNAseq on the Illumina NovaSeq platform. Transcriptomic clustering, linear modeling, differential expression (DE), and gene set enrichment analyses were run using the R packages Seurat, DESeq2, fGSEA, and GSVA. Top DE genes were selected based on P-values <0.05 and log2-fold-change >0.5, comparing MRD+ and MRD6 populations. Results: Within the intention-to-treat (ITT) population after a median observation time of 65.4 months, pts with MRD6 had a significantly longer PFS than pts who had MRD4/MRD5 (A). Pre-treatment RNAseq data were available for 405 of the 432 pts in the ITT population (202 Clb-Obi, 203 Ven-Obi), and at relapse for 41 pts (14 Clb-Obi and 27 Ven-Obi). The pre-treatment transcriptomic profile correlated with the IGHV status, trisomy 12, and del13q (B). No clustering according to MRD status was observed, suggesting that individual pathways/genes rather than global differences are associated with MRD response. Individual gene-level analysis of pre-treatment cohorts showed that MRD+ status was associated with resistance markers such as multi-drug response (MDR) gene or ABCB1, but MRD6 was associated with pro-apoptotic BCL2L11 (BIM) (C). Hallmark apoptotic pathways (P53 and Apoptosis), as well as canonical oncogenic pathways (MYC, mTORC1, TNFɑ/NFκB), were enriched in MRD6 pts in both Ven-Obi and Clb-Obi-treated pts (D). In contrast, inflammatory pathway gene sets (Inflammatory response, IFNγ response, IL2/STAT5) were enriched in MRD+ pts in the Ven-Obi arm, suggesting their role in Ven resistance. Gene sets enriched at progression compared to baseline were mostly related to cell proliferation and oncogenic signaling (E). Moreover, in a GSVA analysis, inflammatory pathway gene sets were also markedly upregulated at progression compared to baseline, providing an orthogonal validation that inflammatory signaling might be associated with resistance to venetoclax therapy (Fig F). Common leading edge genes included IL2RB, LCP2, BST2, IRF7, CASP3, CD86, IRF8, and NCOA3. Image:Summary/Conclusion: This analysis of a large, prospective CLL RNAseq dataset confirms that global transcriptomic profiles cluster according to IGHV, trisomy 12 and del13q. Response and non-response to therapy, as assessed by NGS-based MRD status, was associated with a distinct transcriptomic profile that was characterized by upregulated oncogenic pathways and inflammatory signaling, respectively. These data suggest possible biological vulnerabilities that could be leveraged to overcome resistance to venetoclax.